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Renewed terrorist penetration of homeland security and U.S. intelligence and military bases has thrown President Obama on the defensive - raising deeply disturbing questions about his policies to keep America safe.

Over the past week or more, in the wake of an attempted bombing of an American jetliner over Detroit on Christmas Day, the president and his advisers have responded with a mass of confusing and contradictory statements that has further shaken public confidence in the administration’s handling of the war on terrorism (a term Mr. Obama hates to use).

It started, in the hours following the attempt to bring down a U.S.-bound airline, with Homeland Security Secretary Janet Napolitano’s statement that the nation’s counterterrorism “system worked,” only to scrap those naive words sometime later and admit the attack had exposed serious failings in our security system. An incredible contradiction by the woman in charge of our homeland defenses.

Mr. Obama’s initial statement, while on vacation in Hawaii, referred to the failed bombing attempt by Umar Farouk Abdulmutallab, the 23-year-old Nigerian trained in Yemen, as an “isolated” act. His erroneous description was scrapped, too, when the president told the nation what had already been widely reported, that this was all part of a carefully planned al Qaeda operation. An even more incredible contradiction.

Even more disturbing was the porous nature of the U.S. homeland’s security and counterterrorism systems that were unable to connect the dots on a long list of signals that numerous security agencies received over many months.

“We did have the information throughout the course of the summer and fall about … plans to carry out attacks,” John O. Brennan, Mr. Obama’s chief counterterrorism adviser, said on Fox News Sunday. “We had snippets of information, we had information about Umar Farouk, but we didn’t have any type of information that really allowed us to identify Mr. Abdulmutallab.”

“We may have had a partial name. We might have had an indication of a Nigerian. But there was nothing that brought it all together,” he said.

In fact, the terror trail of information that various agencies received over the course of many months cried out to be connected and recognized by people whose job it is to do that. Mr. Brennan admitted as much when he said “clearly the system didn’t work,” but pointed to many “bits and pieces of information” but not enough to “map it and attach it to” the young Nigerian radical, who had been trained for his bombing mission by al Qaeda in the Arabian Peninsula, where he was referred to as “Brother Umar Farouk the Nigerian.”

Intelligence intercepts were coming in last summer from Yemen that revealed an al Qaeda plot built around “a Nigerian” being trained for a bombing attack, though Mr. Abdulmutallab’s name had not entered the data base reports until his father notified embassy officials that his son was working with extremists. That report alone was the smoking gun that would have connected him to the earlier intercepts.

It is now clear that had this information been put together, Mr. Abdulmutallab would have been put on a watch list that would have prevented him from getting onboard Northwest Airlines flight 253.

America came within milliseconds of another deadly terrorist attack, but the failed attempt has renewed bothersome questions about the Obama administration’s mishandling of homeland security safeguards and the larger war on terrorism.

Among them: Why are we closing down Guantanamo Bay and moving terrorists to prison facilities here in the U.S.? Why are we sending many of them to terrorism breeding grounds where they have rejoined al Qaeda training camps? Mr. Obama has released 42, including seven who were sent home to Yemen. Why are we giving terrorists the privileges and rights of our civilian court system where their cases will likely go on for years though an unending legal process, followed a string of appeals?

Mr. Brennan, using Mr. Obama’s arguments for closing Guantanamo, says it has become “a propaganda tool for al Qaeda,” as if moving the terrorists there to U.S. prisons here would effectively prevent al Qaeda from making this specious claim.

The administration’s botched handling of this latest bomb plot, revealing numerous counterterrorism agencies asleep at the switch, and its policy of giving terrorists the full benefits of our criminal justice system has alarmed the American people - as it should. His job approval polls have fallen into the 40s this week.

Perhaps the last straw was Mr. Brennan’s claim Sunday that Mr. Abdulmutallab would be given the chance to win a plea agreement if he agrees to tell us what he knows about al Qaeda’s terrorist operations in Yemen.

Mr. Abdulmutallab’s “lawyers recognize that there is advantage to talking to us in terms of plea agreements, [and] we’re going to pursue that,” he said on NBC’s “Meet The Press.”

So the man who almost snuffed out the lives of everyone aboard that airline on Christmas day would be offered a chance to cop a plea. This is Mr. Obama’s war on terrorism.

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